-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_8176827-8453457

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_12551-T1
Valid prediction for GeneMark_model.21321_t
Valid prediction for Augustus_model.g8305.t1
Valid prediction for GlimmerHMM_glimmerT_12540-T1
Valid prediction for snap_scaffold_5-snap.1608-T1
Valid prediction for GeneMark_model.21344_t
Valid prediction for snap_scaffold_5-snap.1618-T1
Valid prediction for snap_scaffold_5-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_12547-T1
Valid prediction for Augustus_model.g8299.t1
Valid prediction for GeneMark_model.21341_t
Valid prediction for GlimmerHMM_glimmerT_12560-T1
Valid prediction for GeneMark_model.21328_t
Valid prediction for CodingQuarry_transcript_52013-T1
Valid prediction for GlimmerHMM_glimmerT_12553-T1
Valid prediction for snap_scaffold_5-snap.1620-T1
Valid prediction for snap_scaffold_5-snap.1596-T1
Valid prediction for GeneMark_model.21353_t
Valid prediction for GlimmerHMM_glimmerT_12542-T1
Valid prediction for GeneMark_model.21336_t
Valid prediction for HiQ_model.g8308.t1
Valid prediction for CodingQuarry_transcript_52014-T1
Valid prediction for GeneMark_model.21326_t
Valid prediction for GeneMark_model.21311_t
Valid prediction for GeneMark_model.21343_t
Valid prediction for GlimmerHMM_glimmerT_12558-T1
Valid prediction for Augustus_model.g8298.t1
Valid prediction for Augustus_model.g8311.t1
Valid prediction for GeneMark_model.21361_t
Valid prediction for GeneMark_model.21350_t
Valid prediction for snap_scaffold_5-snap.1592-T1
Valid prediction for GeneMark_model.21340_t
Valid prediction for snap_scaffold_5-snap.1604-T1
Valid prediction for snap_scaffold_5-snap.1624-T1
Valid prediction for GlimmerHMM_glimmerT_12552-T1
Couldn't classify 187247, 187337
Sorry, prediction pasa_asmbl_44200.p1 fails validation.
(CCC)	 AG	187247-187337	GT	TGG
(TGA)	 AG	187524-187695	GT	AGG
(GTC)	 AG	189506-189766	GT	AGG
(GCT)	 AG	191265-191277	TG	GAT
-recovered pasa_asmbl_44200.p1, terminal, 191265, 191277
-recovered pasa_asmbl_44200.p1, internal, 187247, 187337
-recovered pasa_asmbl_44200.p1, internal, 187524, 187695
-recovered pasa_asmbl_44200.p1, internal, 189506, 189766
Valid prediction for snap_scaffold_5-snap.1625-T1
Valid prediction for Augustus_model.g8313.t1
Valid prediction for snap_scaffold_5-snap.1595-T1
Valid prediction for Augustus_model.g8304.t1
Valid prediction for GlimmerHMM_glimmerT_12564-T1
Valid prediction for CodingQuarry_transcript_52012-T1
Valid prediction for GeneMark_model.21346_t
Valid prediction for GlimmerHMM_glimmerT_12548-T1
Valid prediction for Augustus_model.g8303.t1
Valid prediction for snap_scaffold_5-snap.1610-T1
Valid prediction for GeneMark_model.21358_t
Valid prediction for GlimmerHMM_glimmerT_12566-T1
Valid prediction for snap_scaffold_5-snap.1588-T1
Valid prediction for GeneMark_model.21332_t
Valid prediction for Augustus_model.g8312.t1
Valid prediction for GeneMark_model.21362_t
Valid prediction for GeneMark_model.21370_t
Valid prediction for GeneMark_model.21369_t
Valid prediction for snap_scaffold_5-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_12549-T1
Valid prediction for GeneMark_model.21313_t
Valid prediction for snap_scaffold_5-snap.1616-T1
Valid prediction for GeneMark_model.21365_t
Valid prediction for GeneMark_model.21338_t
Valid prediction for GeneMark_model.21354_t
Valid prediction for snap_scaffold_5-snap.1602-T1
Valid prediction for GeneMark_model.21366_t
Valid prediction for Augustus_model.g8300.t1
Valid prediction for pasa_asmbl_44205.p1
Valid prediction for snap_scaffold_5-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_12556-T1
Valid prediction for HiQ_model.g8314.t1
Valid prediction for snap_scaffold_5-snap.1598-T1
Valid prediction for snap_scaffold_5-snap.1594-T1
Valid prediction for GeneMark_model.21356_t
Valid prediction for snap_scaffold_5-snap.1590-T1
Valid prediction for snap_scaffold_5-snap.1599-T1
Valid prediction for GlimmerHMM_glimmerT_12541-T1
Valid prediction for Augustus_model.g8307.t1
Valid prediction for GlimmerHMM_glimmerT_12565-T1
Valid prediction for GlimmerHMM_glimmerT_12537-T1
Valid prediction for GeneMark_model.21348_t
Valid prediction for GlimmerHMM_glimmerT_12561-T1
Valid prediction for GeneMark_model.21323_t
Couldn't classify 225421, 225607
Sorry, prediction pasa_asmbl_44207.p1 fails validation.
(TAT)	 AG	225421-225607	GT	TGG
(GCC)	 AG	225747-225862	GT	AGG
(GTG)	 AG	226544-226653	GT	GAG
(TGG)	 AG	226828-226970	GT	CAG
(ATT)	 AG	227083-227171	GT	CAG
(GTA)	 AG	227393-227517	GT	CAG
(AAG)	 AG	227864-228021	GT	GGG
(GTC)	 AG	228305-228456	CT	GAC
-recovered pasa_asmbl_44207.p1, terminal, 228305, 228456
-recovered pasa_asmbl_44207.p1, internal, 225421, 225607
-recovered pasa_asmbl_44207.p1, internal, 225747, 225862
-recovered pasa_asmbl_44207.p1, internal, 226544, 226653
-recovered pasa_asmbl_44207.p1, internal, 226828, 226970
-recovered pasa_asmbl_44207.p1, internal, 227083, 227171
-recovered pasa_asmbl_44207.p1, internal, 227393, 227517
-recovered pasa_asmbl_44207.p1, internal, 227864, 228021
Valid prediction for GeneMark_model.21359_t
Valid prediction for Augustus_model.g8306.t1
Valid prediction for snap_scaffold_5-snap.1623-T1
Valid prediction for GeneMark_model.21330_t
Valid prediction for snap_scaffold_5-snap.1626-T1
Valid prediction for snap_scaffold_5-snap.1613-T1
Valid prediction for GeneMark_model.21315_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.21364_t
Valid prediction for snap_scaffold_5-snap.1628-T1
Valid prediction for Augustus_model.g8316.t1
Valid prediction for snap_scaffold_5-snap.1605-T1
Valid prediction for GeneMark_model.21324_t
Valid prediction for snap_scaffold_5-snap.1629-T1
Valid prediction for GeneMark_model.21320_t
Valid prediction for GlimmerHMM_glimmerT_12554-T1
Valid prediction for GeneMark_model.21337_t
Valid prediction for GeneMark_model.21360_t
Valid prediction for GlimmerHMM_glimmerT_12568-T1
Valid prediction for GlimmerHMM_glimmerT_12543-T1
Valid prediction for snap_scaffold_5-snap.1607-T1
Valid prediction for GeneMark_model.21373_t
Valid prediction for GlimmerHMM_glimmerT_12539-T1
Valid prediction for GeneMark_model.21327_t
Valid prediction for GeneMark_model.21331_t
Valid prediction for snap_scaffold_5-snap.1597-T1
Valid prediction for snap_scaffold_5-snap.1630-T1
Valid prediction for snap_scaffold_5-snap.1609-T1
Valid prediction for GeneMark_model.21333_t
Valid prediction for GeneMark_model.21352_t
Valid prediction for GeneMark_model.21312_t
Valid prediction for GeneMark_model.21319_t
Valid prediction for GlimmerHMM_glimmerT_12557-T1
Valid prediction for GlimmerHMM_glimmerT_12567-T1
Valid prediction for snap_scaffold_5-snap.1612-T1
Valid prediction for GeneMark_model.21345_t
Valid prediction for snap_scaffold_5-snap.1611-T1
Valid prediction for GeneMark_model.21347_t
Valid prediction for GlimmerHMM_glimmerT_12570-T1
Valid prediction for GeneMark_model.21329_t
Couldn't classify 73545, 73656
Couldn't classify 75501, 75625
Sorry, prediction pasa_asmbl_45588.p1 fails validation.
(GAT)	 GG	73545-73656	GT	GGG
(AGA)	 AG	74404-74507	GT	GGG
(CAC)	 AG	74608-74694	GT	AGG
(TAT)	 AG	74812-74946	GT	AGG
(GTA)	 AG	75095-75172	GT	CTG
(GTG)	 AG	75281-75383	GT	ATG
(ATG)	 AG	75501-75625	GG	ATG
-recovered pasa_asmbl_45588.p1, internal, 74404, 74507
-recovered pasa_asmbl_45588.p1, internal, 74608, 74694
-recovered pasa_asmbl_45588.p1, internal, 74812, 74946
-recovered pasa_asmbl_45588.p1, internal, 75095, 75172
-recovered pasa_asmbl_45588.p1, internal, 75281, 75383
Valid prediction for GeneMark_model.21310_t
Valid prediction for GlimmerHMM_glimmerT_12538-T1
Valid prediction for GeneMark_model.21371_t
Valid prediction for GeneMark_model.21357_t
Valid prediction for snap_scaffold_5-snap.1619-T1
Valid prediction for GlimmerHMM_glimmerT_12550-T1
Valid prediction for GeneMark_model.21367_t
Valid prediction for GeneMark_model.21363_t
Valid prediction for GeneMark_model.21334_t
Valid prediction for Augustus_model.g8309.t1
Valid prediction for GeneMark_model.21317_t
Valid prediction for snap_scaffold_5-snap.1627-T1
Valid prediction for snap_scaffold_5-snap.1622-T1
Valid prediction for snap_scaffold_5-snap.1600-T1
Valid prediction for snap_scaffold_5-snap.1589-T1
Valid prediction for GeneMark_model.21368_t
Valid prediction for GeneMark_model.21325_t
Valid prediction for GeneMark_model.21314_t
Valid prediction for Augustus_model.g8310.t1
Valid prediction for snap_scaffold_5-snap.1614-T1
Valid prediction for GlimmerHMM_glimmerT_12569-T1
Valid prediction for GeneMark_model.21322_t
Valid prediction for snap_scaffold_5-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_12562-T1
Valid prediction for GeneMark_model.21351_t
Valid prediction for GlimmerHMM_glimmerT_12545-T1
Valid prediction for Augustus_model.g8302.t1
Valid prediction for Augustus_model.g8315.t1
Couldn't classify 76170, 76362
Sorry, prediction pasa_asmbl_45587.p2 fails validation.
(GAC)	 CA	76170-76362	GT	AGG
(GTG)	 AG	76548-76657	AA	GAA
-recovered pasa_asmbl_45587.p2, terminal, 76548, 76657
Valid prediction for GlimmerHMM_glimmerT_12555-T1
Valid prediction for GlimmerHMM_glimmerT_12563-T1
Valid prediction for GlimmerHMM_glimmerT_12544-T1
Valid prediction for snap_scaffold_5-snap.1617-T1
Valid prediction for snap_scaffold_5-snap.1593-T1
Valid prediction for GeneMark_model.21318_t
Valid prediction for Augustus_model.g8317.t1
Valid prediction for GlimmerHMM_glimmerT_12559-T1
Valid prediction for snap_scaffold_5-snap.1603-T1
Valid prediction for GeneMark_model.21355_t
Valid prediction for Augustus_model.g8301.t1
Valid prediction for GeneMark_model.21349_t
Valid prediction for GeneMark_model.21335_t
Valid prediction for snap_scaffold_5-snap.1621-T1
Valid prediction for GeneMark_model.21372_t
Valid prediction for GeneMark_model.21342_t
Valid prediction for GeneMark_model.21339_t
Valid prediction for GeneMark_model.21316_t
Valid prediction for GlimmerHMM_glimmerT_12546-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18387, rend_intergenic: 16855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43310, rend_intergenic: 41970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47157, rend_intergenic: 43316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48490, rend_intergenic: 47950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60755, rend_intergenic: 50982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93591, rend_intergenic: 92312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101204, rend_intergenic: 98094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103192, rend_intergenic: 101409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125759, rend_intergenic: 111962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130072, rend_intergenic: 128638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134797, rend_intergenic: 130271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147306, rend_intergenic: 136220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150822, rend_intergenic: 147353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151287, rend_intergenic: 150954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155074, rend_intergenic: 152089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191399, rend_intergenic: 183407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 276631
-exon list size: 689


building trellis

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78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 18387, rend_intergenic: 16855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43310, rend_intergenic: 41970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47157, rend_intergenic: 43316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48490, rend_intergenic: 47950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60755, rend_intergenic: 50982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93591, rend_intergenic: 92312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101204, rend_intergenic: 98094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103192, rend_intergenic: 101409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125759, rend_intergenic: 111962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130072, rend_intergenic: 128638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134797, rend_intergenic: 130271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147306, rend_intergenic: 136220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150822, rend_intergenic: 147353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151287, rend_intergenic: 150954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155074, rend_intergenic: 152089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191399, rend_intergenic: 183407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13943
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 266543 - 276631
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support